"Dogmatic" P Systems

In this work we propose a variant of P systems based on the Central Dogma of Molecular Biology which establishes the transformation of DNA strands into protein products by applying different string transformation such as transductions and transcriptions. We introduce a new kind of worm object rules to carry out transducion operations. Finally, we establish the universality of the proposed model by simulating Iterated finite state sequential transducers (IFTs)

Iterated uniform finite-state transducers

A deterministic iterated uniform finite-state transducer (for short, iufst) operates the same length-preserving transduction on several left-to-right sweeps. The first sweep occurs on the input string, while any other sweep processes the output of the previous one. We focus on constant sweep bounded iufsts. We study their descriptional power vs. deterministic finite automata, and the state cost of implementing language operations. Then, we focus on non-constant sweep bounded iufsts, showing a nonregular language hierarchy depending on sweep complexity

Families of languages encoded by SN P systems

[EN] In this work, we propose the study of SN P systems as classical information encoders. By taking the spike train of an SN P system as a (binary) source of information, we can obtain different languages according to a previously defined encoding alphabet. We provide a characterization of the language families generated by the SN P systems in this way. This characterization depends on the way we define the encoding scheme: bounded or not bounded and, in the first case, with one-to-one or non injective encodings. Finally, we propose a network topology in order to define a cascading encoder.Sempere Luna, JM. (2018). Families of languages encoded by SN P systems. Lecture Notes in Computer Science. 10725:262-269. https://doi.org/10.1007/978-3-319-73359-3_17S26226910725Chen, H., Freund, R., Ionescu, M., Păun, G., Pérez-Jiménez, M.J.: On string languages generated by spiking neural P systems. Fundam. Inf. 75(1–4), 141–162 (2007)Chen, H., Ionescu, M., Păun, A., Păun, G., Popa, B.: On trace languages generated by spiking neural P systems. In: Eighth International Workshop on Descriptional Complexity of Formal Systems (DCFS 2006), Las Cruces, New Mexico, USA, pp. 94–105, 21–23 June 2006Csuhaj-Varjú, E., Vaszil, G.: On counter machines versus dP automata. In: Alhazov, A., Cojocaru, S., Gheorghe, M., Rogozhin, Y., Rozenberg, G., Salomaa, A. (eds.) CMC 2013. LNCS, vol. 8340, pp. 138–150. Springer, Heidelberg (2014). https://doi.org/10.1007/978-3-642-54239-8_11Ibarra, O.H., Leporati, A., Păun, A., Woodworth, S.: Spiking neural P systems. In: Păun, G., Rozenberg, G., Salomaa, A. (eds.) The Oxford Handbook of Membrane Computing, Oxford University Press (2010)Ionescu, M., Păun, G., Yokomori, T.: Spiking neural P systems. Fundam. Inf. 71(2–3), 279–308 (2006)Manca, V.: On the generative power of iterated transduction. In: Ito, M., Păun, G., Yu, S. (eds.) Words, Semigroups, and Transductions, pp. 315–327. World Scientific (2001)Manca, V., Martín-Vide, C., Păun, G.: New computing paradigms suggested by DNA computing: computing by carving. BioSystems 52, 47–54 (1999)Păun, G.: Membrane Computing. An Introduction. Springer, Heidelberg (2002). https://doi.org/10.1007/978-3-642-56196-2Păun, G., Pérez-Jiménez, M.J., Rozenberg, G.: Spike trains in spiking neural P systems. Int. J. Found. Comput. Sci. 17(4), 975–1002 (2006)Rozenberg, G., Salomaa, A. (eds.): Handbook of Formal Languages, vol. 3. Springer, Heidelberg (1997). https://doi.org/10.1007/978-3-642-59136-

MSO definable string transductions and two-way finite state transducers

String transductions that are definable in monadic second-order (mso) logic (without the use of parameters) are exactly those realized by deterministic two-way finite state transducers. Nondeterministic mso definable string transductions (i.e., those definable with the use of parameters) correspond to compositions of two nondeterministic two-way finite state transducers that have the finite visit property. Both families of mso definable string transductions are characterized in terms of Hennie machines, i.e., two-way finite state transducers with the finite visit property that are allowed to rewrite their input tape.Comment: 63 pages, LaTeX2e. Extended abstract presented at 26-th ICALP, 199

Automata-based Analysis of Recursive Cryptographic Protocols

Cryptographic protocols can be divided into (1) protocols where the protocol steps are simple from a computational point of view and can thus be modeled by simple means, for instance, single rewrite rules---we call these protocols non-looping---and (2) protocols, such as group protocols, where the protocol steps are complex and typically involve an iterative or recursive computation---we call them recursive. While many results on the decidability of security are known for non-looping protocols, only little is known for recursive protocols. In this paper, we prove decidability of security (w.r.t.~the standard Dolev-Yao intruder) for a core class of recursive protocols and undecidability for several extensions. The key ingredient of our protocol model are specifically designed tree transducers which work over infinite signatures and have the ability to generate new constants (which allow us to mimic key generation). The decidability result is based on an automata-theoretic construction which involves a new notion of regularity, designed to work well with the infinite signatures we use

P automata revisited

We continue here the investigation of P automata, in their non-extended case, a class of devices which characterize non-universal family of languages. First, a recent conjecture is confirmed: any recursively enumerable language is obtained from a language recognized by a P automaton, to which an initial (arbitrarily large) string is added. Then, we discuss possibilities of extending P automata, following suggestions from string finite automata. For instance, automata with a memory (corresponding to push-down automata) are considered and their power is briefly investigated, as well as some closure properties of the family of languages recognized by P automata. In the context, a brief survey of results about P and dP automata (a distributed version of P automata) is provided, and several further research topics are formulated.Junta de Andalucía P08-TIC-0420

Tree transducers, L systems, and two-way machines

A relationship between parallel rewriting systems and two-way machines is investigated. Restrictions on the “copying power” of these devices endow them with rich structuring and give insight into the issues of determinism, parallelism, and copying. Among the parallel rewriting systems considered are the top-down tree transducer; the generalized syntax-directed translation scheme and the ETOL system, and among the two-way machines are the tree-walking automaton, the two-way finite-state transducer, and (generalizations of) the one-way checking stack automaton. The. relationship of these devices to macro grammars is also considered. An effort is made .to provide a systematic survey of a number of existing results

Forgotten Islands of Regularity in Phonology

Open access publication of this volume supported by National Research, Development and Innovation Office grant NKFIH #120145 `Deep Learning of Morphological Structure'.Giving birth to Finite State Phonology is classically attributed to Johnson (1972), and Kaplan and Kay (1994). However, there is an ear- lier discovery that was very close to this achievement. In 1965, Hennie presented a very general sufficient condition for regularity of Turing machines. Although this discovery happened chronologically before Generative Phonology (Chomsky and Halle, 1968), it is a mystery why its relevance has not been realized until recently (Yli-Jyrä, 2017). The antique work of Hennie provides enough generality to advance even today’s frontier of finite-state phonology. First, it lets us construct a finite-state transducer from any grammar implemented by a tightly bounded one- tape Turing machine. If the machine runs in o(n log n), the construction is possible, and this case is reasonably decidable. Second, it can be used to model the regularity in context-sensitive derivations. For example, the suffixation in hunspell dictionaries (Németh et al., 2004) corresponds to time-bounded two-way computations performed by a Hennie machine. Thirdly, it challenges us to look for new forgotten islands of regularity where Hennie’s condition does not necessarily hold.Hennie presented a very general sufficient condition for regularity of Turing machines. This happened chronologically before Generative Phonology (Chomsky & Halle 1968) and the related finite-state research (Johnson 1972; Kaplan & Kay 1994). Hennie’s condition lets us (1) construct a finite-state transducer from any grammar implemented by a linear-time Turing machine, and (2) to model the regularity in context-sensitive derivations. For example, the suffixation in hunspell dictionaries (Németh et al. 2004) corresponds to time-bounded two way computations performed by a Hennie machine. Furthermore, it challenges us to look for new forgotten islands of regularity where Hennie’s condition does not necessarily hold.Peer reviewe